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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaggcttggattcttcactatttgcgttgcatgtgatagcatgattttctaaaccgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG

Basic information

species Arabidopsis thaliana
transcript AT5G25100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 4
gtaagtaggct--tggattcttcactatttgc-gttgcatgtgatagcatgattttctaaac---cgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG
||| |     |  |  ||    || |  ||   ||||    ||  | |||| |||  |   |   | || ||   ||  ||||||||| ||| | ||||||||||| ||||| || ||||| || ||||||  |||||||||||||| || ||| ||  |||| || |||||||| |||||||
gtatgctctttattttataggacaatgcttattgttgtgaatgcca-catgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACGCTAACTGAATCTGCTAGAATTGTGGGCTTTGAGG

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 4
gtaagtaggct--tggattcttcactatttgc-gttgcatgtgatagcatgattttctaaac---cgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG
||| |     |  |  |||   || | |||   ||||    ||  | |||| |||  |   |   | || ||   ||  ||||||||| ||| | ||||||||||| ||||| || ||||| || ||||||  ||||||||||||||  |  || ||  |||| || |||||||| ||||| |
gtatgctctttattttattggacaatgtttattgttgtgaatgcca-catgttttcttgtgcttactttgttgaaatacacagAGCAAGGAGGAGAAGTATTTTATTCACAACCATTTGGCTTTTACTGTCAAGTATCATAGAGATACACTTACTGAATCTGCTAGAATTGTGGGCTTTGAAG

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtaggcttgg-attcttcact--atttgcgttgcatgtgata-gcatgattttc-taaac---cgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG
||||||||  | |  |||  | ||   | |   ||||       |  ||||| ||||| |   |   | ||||    || |||||| ||| ||  | ||||||||||| |||||||| |||  ||| || |||  || ||||| |||| ||||||| ||  | ||||||||||||||||||||||
gtaagtagattagctattagtaacaggaatctagttgttgccattgtgcatgcttttcatttgcttactttataattatatacagAACAAGGAAGAGAAGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125174564|gb|EL195306.1|EL195306
EST:     TTGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGG                         AGCAAAGAGCAAAAGTATTTTATGCA
genomic: TTGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGGgtaagtaggc ... gcatttacagAGCAAAGAGCAAAAGTATTTTATGCA
EST: gi|164169290|gb|ES026612.1|ES026612
EST:     TGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGG                         AGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCAC
genomic: TGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGGgtaagtaggc ... gcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCAC
EST: gi|125276754|gb|EL290839.1|EL290839
EST:     CTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGG                         AGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTG
genomic: CTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGGgtaagtaggc ... gcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTG
EST: gi|86072801|gb|DR368558.1|DR368558
EST:     TTGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGG                         AGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGG
genomic: TTGTGTATCAGCTAGGATATCATGTTGGTCTTAAAGGCCAGTATGAAGGGgtaagtaggc ... gcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttgcgttgcatgtgatagcatgattttctaaaccgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG
                             ttctaaa  putative branch site (score: 2)
                          attttctaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaggcttggattcttcactatttgcgttgcatgtgatagcatgattttctaaaccgttatttgcatttacagAGCAAAGAGCAAAAGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC